United's hopes of avoiding relegation were hit at City's Academy Stadium when Lorenzo Gonzalez put City ahead after four minutes.
But, in first-half stoppage time, Boonen (pictured) nodded in Callum Gribbin's free-kick.
City, for whom Benjamin Mendy made a return after a seven-month injury absence, dominated after the break but Kieran O'Hara's saves for United earned them a vital point.
United, on 19 points, climb above Sunderland, who have a match in hand, on goal difference. But they will be relegated if Derby County beat West Ham United next week.
City are eighth on 27 points.
Man City: 2 May v Spurs (A) PL2
Man Utd: 20 Apr v Everton (H) PL2